import java.awt.Color;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
import java.util.Map;
*/
public class PymolCommands extends StructureCommandsBase
{
- private static final StructureCommand CLOSE_PYMOL = new StructureCommand("quit");
+ // https://pymol.org/dokuwiki/doku.php?id=command:zoom
+ // not currently documented on
+ // https://pymolwiki.org/index.php/Category:Commands
+ private static final StructureCommand FOCUS_VIEW = new StructureCommand(
+ "zoom");
- private static final StructureCommand COLOUR_BY_CHAIN = new StructureCommand("spectrum", "chain");
+ // https://pymolwiki.org/index.php/Quit
+ private static final StructureCommand CLOSE_PYMOL = new StructureCommand(
+ "quit");
- private static final List<StructureCommandI> COLOR_BY_CHARGE = new ArrayList<>();
+ // not currently documented on
+ // https://pymolwiki.org/index.php/Category:Commands
+ private static final StructureCommand COLOUR_BY_CHAIN = new StructureCommand(
+ "spectrum", "chain");
- private static final List<StructureCommandI> SHOW_BACKBONE = new ArrayList<>();
+ private static final List<StructureCommandI> COLOR_BY_CHARGE = Arrays
+ .asList(new StructureCommand("color", "white", "*"),
+ new StructureCommand("color", "red", "resn ASP resn GLU"),
+ new StructureCommand("color", "blue",
+ "resn LYS resn ARG"),
+ new StructureCommand("color", "yellow", "resn CYS"));
- static {
- COLOR_BY_CHARGE.add(new StructureCommand("color", "white", "*"));
- COLOR_BY_CHARGE
- .add(new StructureCommand("color", "red", "resn ASP resn GLU"));
- COLOR_BY_CHARGE.add(
- new StructureCommand("color", "blue", "resn LYS resn ARG"));
- COLOR_BY_CHARGE
- .add(new StructureCommand("color", "yellow", "resn CYS"));
- SHOW_BACKBONE.add(new StructureCommand("hide", "everything"));
- SHOW_BACKBONE.add(new StructureCommand("show", "ribbon"));
- }
+ private static final List<StructureCommandI> SHOW_BACKBONE = Arrays
+ .asList(new StructureCommand("hide", "everything"),
+ new StructureCommand("show", "ribbon"));
@Override
public StructureCommandI colourByChain()
@Override
public StructureCommandI focusView()
{
- // https://pymol.org/dokuwiki/doku.php?id=command:zoom
- // not currently documented on https://pymolwiki.org/index.php/Category:Commands
- return new StructureCommand("zoom");
+ return FOCUS_VIEW;
}
@Override
{
chains.append(" chain ").append(chain);
}
- commands.add(new StructureCommand("show", "cartoon", chains.toString()));
+ commands.add(
+ new StructureCommand("show", "cartoon", chains.toString()));
return commands;
}
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec)
+ AtomSpecModel atomSpec, AtomSpecType specType)
{
+
// https://pymolwiki.org/index.php/Super
List<StructureCommandI> commands = new ArrayList<>();
- String refAtomsAlphaOnly = getAtomSpec(refAtoms, true);
- String atomSpec2AlphaOnly = getAtomSpec(atomSpec, true);
- commands.add(new StructureCommand("super", refAtomsAlphaOnly,
- atomSpec2AlphaOnly));
+ String refAtomsAlphaOnly = "(" + getAtomSpec(refAtoms, specType)
+ + " and (altloc '' or altloc 'a'))";
+ String atomSpec2AlphaOnly = "(" + getAtomSpec(atomSpec, specType)
+ + " and (altloc '' or altloc 'a'))";
+ // pair_fit mobile -> reference
+ // crashes when undo is enabled on 2.5.2 (incentive)
+ commands.add(new StructureCommand("undo_disable"));
+ commands.add(new StructureCommand("pair_fit", atomSpec2AlphaOnly,
+ refAtomsAlphaOnly));
+ commands.add(new StructureCommand("undo_enable"));
/*
* and show superposed residues as cartoon
*/
- String refAtomsAll = getAtomSpec(refAtoms, false);
- String atomSpec2All = getAtomSpec(atomSpec, false);
+ String refAtomsAll = getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY);
+ String atomSpec2All = getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY);
commands.add(new StructureCommand("show", "cartoon",
refAtomsAll + " " + atomSpec2All));
* @see https://pymolwiki.org/index.php/Selection_Macros
*/
@Override
- public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(64);
boolean first = true;
}
}
sb.append("/");
- if (alphaOnly)
+ if (specType == AtomSpecType.ALPHA)
{
sb.append("CA");
}
+ if (specType == AtomSpecType.PHOSPHATE)
+ {
+ sb.append("P");
+ }
}
}
return sb.toString();
final AtomSpecModel colourData = colourMap.get(colour);
commands.add(getColourCommand(colourData, colour));
}
-
+
return commands;
}
* @return
*/
protected StructureCommandI setAttribute(String attributeName,
- String attributeValue,
- AtomSpecModel atomSpecModel)
+ String attributeValue, AtomSpecModel atomSpecModel)
{
StringBuilder sb = new StringBuilder(128);
sb.append("p.").append(attributeName).append("='")
.append(attributeValue).append("'");
- String atomSpec = getAtomSpec(atomSpecModel, false);
+ String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
return new StructureCommand("iterate", atomSpec, sb.toString());
}
for (String featureType : featureMap.keySet())
{
String attributeName = makeAttributeName(featureType);
-
+
/*
* todo: clear down existing attributes for this feature?
*/
// commands.add(new StructureCommand("iterate", "all",
// "p."+attributeName+"='None'"); //?
-
+
Map<Object, AtomSpecModel> values = featureMap.get(featureType);
for (Object value : values.keySet())
{
commands.add(cmd);
}
}
-
+
return commands;
}